/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.dev;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.data.seg.SegmentedAsciiDataSet;
import org.broad.igv.dev.db.DBManager;
import org.broad.igv.dev.db.DBProfile;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.io.File;
import static junit.framework.Assert.*;
/**
* Test of our multi-purpose reader class
* User: jacob
* Date: 2012-Oct-23
*/
public class SegmentedReaderTest extends AbstractHeadlessTest {
private SegmentedAsciiDataSet loadSegFile() throws Exception {
String filePath = TestUtils.DATA_DIR + "seg/canFam2_hg18.seg";
ResourceLocator locator = new ResourceLocator(filePath);
SegmentedReader reader = new SegmentedReader(locator);
SegmentedAsciiDataSet ds = reader.loadFromFile();
assertEquals(18, ds.getChromosomes().size());
return ds;
}
@Test
public void testLoadSegFile() throws Exception {
SegmentedAsciiDataSet ds = loadSegFile();
assertNotNull(ds);
assertFalse(ds.getChromosomes().isEmpty());
}
@Test
public void testLoadSegDB() throws Exception {
SegmentedAsciiDataSet ds = loadSegDB();
assertNotNull(ds);
assertFalse(ds.getChromosomes().isEmpty());
}
private SegmentedAsciiDataSet loadSegDB() throws Exception {
String host = (new File(TestUtils.DATA_DIR)).getAbsolutePath();
String path = "seg/canFam2_hg18.db";
String url = DBManager.createConnectionURL("sqlite", host, path, null);
ResourceLocator locator = new ResourceLocator(url);
String tableName = "canFam2";
SegmentedReader reader = new SegmentedReader(locator);
DBProfile.DBTable table = DBProfile.DBTable.build(locator, tableName);
SegmentedAsciiDataSet ds = reader.loadFromDB(table);
return ds;
}
@Test
public void compareFileDB() throws Exception {
SegmentedAsciiDataSet fileDS = loadSegFile();
SegmentedAsciiDataSet dbDS = loadSegDB();
assertEquals(fileDS.getChromosomes(), dbDS.getChromosomes());
assertEquals(fileDS.getSampleNames(), dbDS.getSampleNames());
}
//Scratch work for testing loading from local mysql db
public void testLoadMySQL() throws Exception {
String url = DBManager.createConnectionURL("mysql", "calcium", "igv_nobel_dev", null);
ResourceLocator locator = new ResourceLocator(url);
locator.setUsername("igv_nobel_dev");
locator.setPassword("nottherealpassword");
String tableName = "CNV";
DBProfile.DBTable table = DBProfile.DBTable.build(locator, tableName);
SegmentedReader reader = new SegmentedReader(locator);
SegmentedAsciiDataSet ds = reader.loadFromDB(table);
}
}